I don't think you're going to be able to fix this without modifying CGI::Session.

Basically, what the "active statement handle" warning means is that the database connection is going away while there's a query still active which might have results which haven't been retrieved yet. Some database drivers are smart enough to recognize that a query has had all results retrieved when the last row is fetched. Others don't recognize this until you attempt to fetch a row that isn't there. You are apparently either using one which falls into the latter category (more likely) or the session table has gotten messed up such that the id you're testing with has multiple a_session records.

The reason that switching to prepare would fix this is that it allows $sth to be destroyed when it falls out of scope at the end of the sub. prepare_cached stores a second copy of the statement handle in case that same query is prepared again later; it is this second (cached) copy which is still active when your database connection goes away and triggers the warning.

A better solution, IMO, would be to continue using prepare_cached and add the line $sth->finish; immediately after my ($row) = $sth->fetchrow_array();. This will tell the database engine that you're done with the query's results even if it thinks there may still be additional rows to return.

I think i found solution.
The problem is that DBD::SQlite->disconnect() method execute
sqlite3_close() function.
This function return SQLITE_BUSY in case if there are any active statement.
From API:
"Applications should finalize all prepared statements and close all
BLOBs associated with the sqlite3 object prior to attempting to close
the sqlite3 object."
Currently DBD::SQLite can finalize statements only via DESTROY method.
In simplest case you can always use "undef $sth" or wait untill it
goes out of scope
which will finalize statement.
But if you prepared statement via cache (prepare_cached) it will not
work for you,
because statement is till inside DBI cache. In this case we can call
DESTROY on our cached statement only via DESTROY for database handler.
And we can achieve it by "undef $dbh".
"undef $dbh" - will close all cached statements and close database
without any errors.
Conclusion: avoid using $dbh->disconnect() for DBD::SQLite, instead
use "undef $dbh".